scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scitex/__init__.py +19 -8
- scitex/__main__.py +2 -1
- scitex/__version__.py +1 -1
- scitex/_optional_deps.py +13 -20
- scitex/ai/__init__.py +5 -0
- scitex/ai/_gen_ai/_Anthropic.py +3 -1
- scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
- scitex/ai/_gen_ai/_DeepSeek.py +1 -1
- scitex/ai/_gen_ai/_Google.py +3 -2
- scitex/ai/_gen_ai/_Llama.py +4 -2
- scitex/ai/_gen_ai/_OpenAI.py +3 -1
- scitex/ai/_gen_ai/_PARAMS.py +1 -0
- scitex/ai/_gen_ai/_Perplexity.py +3 -1
- scitex/ai/_gen_ai/__init__.py +1 -0
- scitex/ai/_gen_ai/_format_output_func.py +3 -1
- scitex/ai/classification/CrossValidationExperiment.py +8 -14
- scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
- scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
- scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
- scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
- scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
- scitex/ai/classification/reporters/__init__.py +1 -1
- scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
- scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
- scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
- scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
- scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
- scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
- scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
- scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
- scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
- scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
- scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
- scitex/ai/classification/timeseries/__init__.py +2 -4
- scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
- scitex/ai/clustering/_pca.py +0 -1
- scitex/ai/clustering/_umap.py +1 -2
- scitex/ai/feature_extraction/__init__.py +10 -8
- scitex/ai/feature_extraction/vit.py +0 -1
- scitex/ai/feature_selection/feature_selection.py +3 -8
- scitex/ai/metrics/_calc_conf_mat.py +2 -0
- scitex/ai/metrics/_calc_feature_importance.py +3 -7
- scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
- scitex/ai/metrics/_calc_roc_auc.py +4 -2
- scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
- scitex/ai/metrics/_calc_silhouette_score.py +1 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
- scitex/ai/optim/_optimizers.py +1 -1
- scitex/ai/plt/__init__.py +6 -1
- scitex/ai/plt/_plot_feature_importance.py +1 -3
- scitex/ai/plt/_plot_learning_curve.py +9 -24
- scitex/ai/plt/_plot_optuna_study.py +4 -3
- scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
- scitex/ai/plt/_plot_roc_curve.py +6 -8
- scitex/ai/plt/_stx_conf_mat.py +121 -122
- scitex/ai/sampling/undersample.py +3 -2
- scitex/ai/sklearn/__init__.py +2 -2
- scitex/ai/training/_LearningCurveLogger.py +23 -10
- scitex/ai/utils/_check_params.py +0 -1
- scitex/benchmark/__init__.py +15 -25
- scitex/benchmark/benchmark.py +124 -117
- scitex/benchmark/monitor.py +117 -107
- scitex/benchmark/profiler.py +61 -58
- scitex/bridge/__init__.py +110 -0
- scitex/bridge/_helpers.py +149 -0
- scitex/bridge/_plt_vis.py +529 -0
- scitex/bridge/_protocol.py +283 -0
- scitex/bridge/_stats_plt.py +261 -0
- scitex/bridge/_stats_vis.py +265 -0
- scitex/browser/__init__.py +0 -2
- scitex/browser/auth/__init__.py +0 -0
- scitex/browser/auth/google.py +16 -11
- scitex/browser/automation/CookieHandler.py +2 -3
- scitex/browser/collaboration/__init__.py +3 -0
- scitex/browser/collaboration/auth_helpers.py +3 -1
- scitex/browser/collaboration/collaborative_agent.py +2 -0
- scitex/browser/collaboration/interactive_panel.py +2 -2
- scitex/browser/collaboration/shared_session.py +20 -11
- scitex/browser/collaboration/standard_interactions.py +1 -0
- scitex/browser/core/BrowserMixin.py +12 -30
- scitex/browser/core/ChromeProfileManager.py +9 -24
- scitex/browser/debugging/_browser_logger.py +15 -25
- scitex/browser/debugging/_failure_capture.py +9 -2
- scitex/browser/debugging/_highlight_element.py +15 -6
- scitex/browser/debugging/_show_grid.py +5 -6
- scitex/browser/debugging/_sync_session.py +4 -3
- scitex/browser/debugging/_test_monitor.py +14 -5
- scitex/browser/debugging/_visual_cursor.py +46 -35
- scitex/browser/interaction/click_center.py +4 -3
- scitex/browser/interaction/click_with_fallbacks.py +7 -10
- scitex/browser/interaction/close_popups.py +79 -66
- scitex/browser/interaction/fill_with_fallbacks.py +8 -8
- scitex/browser/pdf/__init__.py +3 -1
- scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
- scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
- scitex/browser/remote/CaptchaHandler.py +109 -96
- scitex/browser/remote/ZenRowsAPIClient.py +91 -97
- scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
- scitex/browser/stealth/HumanBehavior.py +4 -9
- scitex/browser/stealth/StealthManager.py +11 -26
- scitex/capture/__init__.py +17 -17
- scitex/capture/__main__.py +2 -3
- scitex/capture/capture.py +23 -51
- scitex/capture/cli.py +14 -39
- scitex/capture/gif.py +5 -9
- scitex/capture/mcp_server.py +7 -20
- scitex/capture/session.py +4 -3
- scitex/capture/utils.py +18 -53
- scitex/cli/__init__.py +1 -1
- scitex/cli/cloud.py +158 -116
- scitex/cli/config.py +224 -0
- scitex/cli/main.py +41 -40
- scitex/cli/scholar.py +60 -27
- scitex/cli/security.py +14 -20
- scitex/cli/web.py +87 -90
- scitex/cli/writer.py +51 -45
- scitex/cloud/__init__.py +14 -11
- scitex/cloud/_matplotlib_hook.py +6 -6
- scitex/config/README.md +313 -0
- scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
- scitex/config/_ScitexConfig.py +319 -0
- scitex/config/__init__.py +41 -9
- scitex/config/_paths.py +325 -0
- scitex/config/default.yaml +81 -0
- scitex/context/_suppress_output.py +2 -3
- scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
- scitex/db/_BaseMixins/__init__.py +1 -1
- scitex/db/__init__.py +9 -1
- scitex/db/__main__.py +8 -21
- scitex/db/_check_health.py +15 -31
- scitex/db/_delete_duplicates.py +7 -4
- scitex/db/_inspect.py +22 -38
- scitex/db/_inspect_optimized.py +89 -85
- scitex/db/_postgresql/_PostgreSQL.py +0 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
- scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
- scitex/db/_postgresql/__init__.py +1 -1
- scitex/db/_sqlite3/_SQLite3.py +2 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
- scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
- scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
- scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
- scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
- scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
- scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
- scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
- scitex/db/_sqlite3/__init__.py +1 -1
- scitex/db/_sqlite3/_delete_duplicates.py +13 -11
- scitex/decorators/__init__.py +29 -4
- scitex/decorators/_auto_order.py +43 -43
- scitex/decorators/_batch_fn.py +12 -6
- scitex/decorators/_cache_disk.py +8 -9
- scitex/decorators/_cache_disk_async.py +8 -7
- scitex/decorators/_combined.py +19 -13
- scitex/decorators/_converters.py +16 -3
- scitex/decorators/_deprecated.py +32 -22
- scitex/decorators/_numpy_fn.py +18 -4
- scitex/decorators/_pandas_fn.py +17 -5
- scitex/decorators/_signal_fn.py +17 -3
- scitex/decorators/_torch_fn.py +32 -15
- scitex/decorators/_xarray_fn.py +23 -9
- scitex/dev/_analyze_code_flow.py +0 -2
- scitex/dict/_DotDict.py +15 -19
- scitex/dict/_flatten.py +1 -0
- scitex/dict/_listed_dict.py +1 -0
- scitex/dict/_pop_keys.py +1 -0
- scitex/dict/_replace.py +1 -0
- scitex/dict/_safe_merge.py +1 -0
- scitex/dict/_to_str.py +2 -3
- scitex/dsp/__init__.py +13 -4
- scitex/dsp/_crop.py +3 -1
- scitex/dsp/_detect_ripples.py +3 -1
- scitex/dsp/_modulation_index.py +3 -1
- scitex/dsp/_time.py +3 -1
- scitex/dsp/_wavelet.py +0 -1
- scitex/dsp/example.py +0 -5
- scitex/dsp/filt.py +4 -0
- scitex/dsp/utils/__init__.py +4 -1
- scitex/dsp/utils/pac.py +3 -3
- scitex/dt/_normalize_timestamp.py +4 -1
- scitex/errors.py +3 -6
- scitex/etc/__init__.py +1 -1
- scitex/gen/_DimHandler.py +6 -6
- scitex/gen/__init__.py +5 -1
- scitex/gen/_deprecated_close.py +1 -0
- scitex/gen/_deprecated_start.py +5 -3
- scitex/gen/_detect_environment.py +44 -41
- scitex/gen/_detect_notebook_path.py +51 -47
- scitex/gen/_embed.py +1 -1
- scitex/gen/_get_notebook_path.py +81 -62
- scitex/gen/_inspect_module.py +0 -1
- scitex/gen/_norm.py +16 -7
- scitex/gen/_norm_cache.py +78 -65
- scitex/gen/_print_config.py +0 -3
- scitex/gen/_src.py +2 -3
- scitex/gen/_title_case.py +3 -2
- scitex/gen/_to_even.py +8 -8
- scitex/gen/_transpose.py +3 -3
- scitex/gen/misc.py +0 -3
- scitex/gists/_SigMacro_processFigure_S.py +2 -2
- scitex/gists/_SigMacro_toBlue.py +2 -2
- scitex/gists/__init__.py +4 -1
- scitex/git/_branch.py +19 -11
- scitex/git/_clone.py +23 -15
- scitex/git/_commit.py +10 -12
- scitex/git/_init.py +15 -38
- scitex/git/_remote.py +9 -3
- scitex/git/_result.py +3 -0
- scitex/git/_retry.py +2 -5
- scitex/git/_types.py +4 -0
- scitex/git/_validation.py +8 -8
- scitex/git/_workflow.py +4 -4
- scitex/io/__init__.py +2 -1
- scitex/io/_glob.py +2 -2
- scitex/io/_json2md.py +3 -3
- scitex/io/_load.py +6 -8
- scitex/io/_load_cache.py +71 -71
- scitex/io/_load_configs.py +2 -3
- scitex/io/_load_modules/_H5Explorer.py +6 -12
- scitex/io/_load_modules/_ZarrExplorer.py +3 -3
- scitex/io/_load_modules/_bibtex.py +62 -63
- scitex/io/_load_modules/_canvas.py +4 -9
- scitex/io/_load_modules/_catboost.py +7 -2
- scitex/io/_load_modules/_hdf5.py +2 -0
- scitex/io/_load_modules/_image.py +5 -1
- scitex/io/_load_modules/_matlab.py +3 -1
- scitex/io/_load_modules/_optuna.py +0 -1
- scitex/io/_load_modules/_pdf.py +38 -29
- scitex/io/_load_modules/_sqlite3.py +1 -0
- scitex/io/_load_modules/_txt.py +2 -0
- scitex/io/_load_modules/_xml.py +9 -9
- scitex/io/_load_modules/_zarr.py +12 -10
- scitex/io/_metadata.py +76 -37
- scitex/io/_qr_utils.py +18 -13
- scitex/io/_save.py +220 -63
- scitex/io/_save_modules/__init__.py +7 -2
- scitex/io/_save_modules/_bibtex.py +66 -61
- scitex/io/_save_modules/_canvas.py +5 -6
- scitex/io/_save_modules/_catboost.py +2 -2
- scitex/io/_save_modules/_csv.py +4 -4
- scitex/io/_save_modules/_excel.py +5 -9
- scitex/io/_save_modules/_hdf5.py +9 -21
- scitex/io/_save_modules/_html.py +5 -5
- scitex/io/_save_modules/_image.py +105 -8
- scitex/io/_save_modules/_joblib.py +2 -2
- scitex/io/_save_modules/_json.py +51 -6
- scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
- scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
- scitex/io/_save_modules/_matlab.py +2 -2
- scitex/io/_save_modules/_numpy.py +6 -8
- scitex/io/_save_modules/_pickle.py +4 -4
- scitex/io/_save_modules/_plotly.py +3 -3
- scitex/io/_save_modules/_tex.py +23 -25
- scitex/io/_save_modules/_text.py +2 -2
- scitex/io/_save_modules/_yaml.py +9 -9
- scitex/io/_save_modules/_zarr.py +15 -15
- scitex/io/utils/__init__.py +2 -1
- scitex/io/utils/h5_to_zarr.py +173 -155
- scitex/linalg/__init__.py +1 -1
- scitex/linalg/_geometric_median.py +4 -3
- scitex/logging/_Tee.py +5 -7
- scitex/logging/__init__.py +18 -19
- scitex/logging/_config.py +4 -1
- scitex/logging/_context.py +6 -5
- scitex/logging/_formatters.py +2 -3
- scitex/logging/_handlers.py +19 -20
- scitex/logging/_levels.py +9 -17
- scitex/logging/_logger.py +74 -15
- scitex/logging/_print_capture.py +17 -17
- scitex/nn/_BNet.py +1 -3
- scitex/nn/_Filters.py +6 -2
- scitex/nn/_ModulationIndex.py +3 -1
- scitex/nn/_PAC.py +3 -2
- scitex/nn/_PSD.py +0 -1
- scitex/nn/__init__.py +16 -3
- scitex/path/_clean.py +10 -8
- scitex/path/_find.py +1 -1
- scitex/path/_get_spath.py +1 -2
- scitex/path/_mk_spath.py +1 -1
- scitex/path/_symlink.py +5 -10
- scitex/pd/__init__.py +4 -1
- scitex/pd/_force_df.py +24 -24
- scitex/pd/_get_unique.py +1 -0
- scitex/pd/_merge_columns.py +1 -1
- scitex/pd/_round.py +11 -7
- scitex/pd/_to_xy.py +0 -1
- scitex/plt/REQUESTS.md +191 -0
- scitex/plt/__init__.py +185 -87
- scitex/plt/_subplots/_AxesWrapper.py +22 -6
- scitex/plt/_subplots/_AxisWrapper.py +100 -39
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
- scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
- scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
- scitex/plt/_subplots/_FigWrapper.py +93 -60
- scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
- scitex/plt/_subplots/__init__.py +10 -0
- scitex/plt/_subplots/_export_as_csv.py +89 -47
- scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
- scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
- scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
- scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +16 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +17 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +43 -26
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +68 -47
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +52 -64
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +55 -50
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +9 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +4 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +44 -40
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +75 -94
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +17 -15
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +10 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_fillv.py +35 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_heatmap.py +18 -18
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_image.py +24 -18
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_joyplot.py +9 -7
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_line.py +34 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_ci.py +15 -13
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_std.py +12 -10
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_median_iqr.py +15 -13
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_raster.py +11 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_rectangle.py +84 -56
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_scatter_hist.py +35 -32
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_shaded_line.py +46 -30
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_violin.py +51 -51
- scitex/plt/_subplots/_export_as_csv_formatters/_format_text.py +32 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_violin.py +34 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py +44 -37
- scitex/plt/_subplots/_export_as_csv_formatters/verify_formatters.py +91 -74
- scitex/plt/_tpl.py +6 -5
- scitex/plt/ax/_plot/__init__.py +24 -0
- scitex/plt/ax/_plot/_add_fitted_line.py +12 -11
- scitex/plt/ax/_plot/_plot_circular_hist.py +3 -1
- scitex/plt/ax/_plot/_plot_statistical_shaded_line.py +25 -19
- scitex/plt/ax/_plot/_stx_conf_mat.py +6 -3
- scitex/plt/ax/_plot/_stx_ecdf.py +5 -3
- scitex/plt/ax/_plot/_stx_fillv.py +4 -2
- scitex/plt/ax/_plot/_stx_heatmap.py +7 -4
- scitex/plt/ax/_plot/_stx_image.py +7 -5
- scitex/plt/ax/_plot/_stx_joyplot.py +32 -10
- scitex/plt/ax/_plot/_stx_raster.py +26 -11
- scitex/plt/ax/_plot/_stx_rectangle.py +2 -2
- scitex/plt/ax/_plot/_stx_shaded_line.py +15 -11
- scitex/plt/ax/_plot/_stx_violin.py +3 -1
- scitex/plt/ax/_style/_add_marginal_ax.py +6 -4
- scitex/plt/ax/_style/_auto_scale_axis.py +14 -10
- scitex/plt/ax/_style/_extend.py +3 -1
- scitex/plt/ax/_style/_force_aspect.py +5 -3
- scitex/plt/ax/_style/_format_units.py +2 -2
- scitex/plt/ax/_style/_hide_spines.py +5 -1
- scitex/plt/ax/_style/_map_ticks.py +5 -3
- scitex/plt/ax/_style/_rotate_labels.py +5 -4
- scitex/plt/ax/_style/_rotate_labels_v01.py +73 -63
- scitex/plt/ax/_style/_set_log_scale.py +120 -85
- scitex/plt/ax/_style/_set_meta.py +99 -76
- scitex/plt/ax/_style/_set_supxyt.py +33 -16
- scitex/plt/ax/_style/_set_xyt.py +27 -18
- scitex/plt/ax/_style/_share_axes.py +15 -5
- scitex/plt/ax/_style/_show_spines.py +58 -57
- scitex/plt/ax/_style/_style_barplot.py +1 -1
- scitex/plt/ax/_style/_style_boxplot.py +25 -14
- scitex/plt/ax/_style/_style_errorbar.py +0 -0
- scitex/plt/ax/_style/_style_scatter.py +1 -1
- scitex/plt/ax/_style/_style_suptitles.py +3 -3
- scitex/plt/ax/_style/_style_violinplot.py +8 -2
- scitex/plt/color/__init__.py +34 -2
- scitex/plt/color/_add_hue_col.py +1 -0
- scitex/plt/color/_colors.py +0 -1
- scitex/plt/color/_get_colors_from_conf_matap.py +3 -1
- scitex/plt/color/_vizualize_colors.py +0 -1
- scitex/plt/docs/FIGURE_ARCHITECTURE.md +155 -97
- scitex/plt/gallery/README.md +75 -0
- scitex/plt/gallery/__init__.py +29 -0
- scitex/plt/gallery/_generate.py +153 -0
- scitex/plt/gallery/_plots.py +594 -0
- scitex/plt/gallery/_registry.py +153 -0
- scitex/plt/styles/__init__.py +9 -9
- scitex/plt/styles/_plot_defaults.py +62 -61
- scitex/plt/styles/_plot_postprocess.py +126 -77
- scitex/plt/styles/_style_loader.py +0 -0
- scitex/plt/styles/presets.py +43 -18
- scitex/plt/templates/research-master/scitex/vis/gallery/area/fill_between.json +110 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/area/fill_betweenx.json +88 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/area/stx_fill_between.json +103 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/area/stx_fillv.json +106 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/bar.json +92 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/barh.json +92 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/boxplot.json +92 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_bar.json +84 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_barh.json +84 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_box.json +83 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_boxplot.json +93 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_violin.json +91 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_violinplot.json +91 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/categorical/violinplot.json +91 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/contour/contour.json +97 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/contour/contourf.json +98 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/contour/stx_contour.json +84 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/distribution/hist.json +101 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/distribution/hist2d.json +96 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/distribution/stx_ecdf.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/distribution/stx_joyplot.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/distribution/stx_kde.json +93 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/grid/imshow.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/grid/matshow.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_conf_mat.json +83 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_heatmap.json +92 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_image.json +121 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_imshow.json +84 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/line/plot.json +110 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/line/step.json +92 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/line/stx_line.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/line/stx_shaded_line.json +96 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/scatter/hexbin.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/scatter/scatter.json +95 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/scatter/stem.json +92 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/scatter/stx_scatter.json +84 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/special/pie.json +94 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/special/stx_raster.json +109 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/special/stx_rectangle.json +108 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/statistical/errorbar.json +93 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_errorbar.json +84 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_mean_ci.json +96 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_mean_std.json +96 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_median_iqr.json +96 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/vector/quiver.json +99 -0
- scitex/plt/templates/research-master/scitex/vis/gallery/vector/streamplot.json +100 -0
- scitex/plt/utils/__init__.py +29 -2
- scitex/plt/utils/_close.py +8 -3
- scitex/plt/utils/_collect_figure_metadata.py +3031 -265
- scitex/plt/utils/_colorbar.py +15 -17
- scitex/plt/utils/_configure_mpl.py +22 -14
- scitex/plt/utils/_crop.py +60 -27
- scitex/plt/utils/_csv_column_naming.py +123 -72
- scitex/plt/utils/_dimension_viewer.py +7 -19
- scitex/plt/utils/_figure_from_axes_mm.py +70 -16
- scitex/plt/utils/_figure_mm.py +3 -2
- scitex/plt/utils/_get_actual_font.py +5 -4
- scitex/plt/utils/_histogram_utils.py +52 -48
- scitex/plt/utils/_is_valid_axis.py +19 -13
- scitex/plt/utils/_mk_colorbar.py +3 -3
- scitex/plt/utils/_scientific_captions.py +202 -139
- scitex/plt/utils/_scitex_config.py +98 -98
- scitex/plt/utils/_units.py +0 -0
- scitex/plt/utils/metadata/__init__.py +36 -0
- scitex/plt/utils/metadata/_artist_extraction.py +119 -0
- scitex/plt/utils/metadata/_axes_metadata.py +93 -0
- scitex/plt/utils/metadata/_collection_artists.py +292 -0
- scitex/plt/utils/metadata/_core.py +208 -0
- scitex/plt/utils/metadata/_csv_column_extraction.py +186 -0
- scitex/plt/utils/metadata/_csv_hash.py +115 -0
- scitex/plt/utils/metadata/_csv_verification.py +95 -0
- scitex/plt/utils/metadata/_data_linkage.py +263 -0
- scitex/plt/utils/metadata/_dimensions.py +239 -0
- scitex/plt/utils/metadata/_figure_metadata.py +58 -0
- scitex/plt/utils/metadata/_image_text_artists.py +168 -0
- scitex/plt/utils/metadata/_label_parsing.py +82 -0
- scitex/plt/utils/metadata/_legend_extraction.py +120 -0
- scitex/plt/utils/metadata/_line_artists.py +367 -0
- scitex/plt/utils/metadata/_line_semantic_handling.py +173 -0
- scitex/plt/utils/metadata/_patch_artists.py +211 -0
- scitex/plt/utils/metadata/_plot_content.py +26 -0
- scitex/plt/utils/metadata/_plot_type_detection.py +184 -0
- scitex/plt/utils/metadata/_precision.py +134 -0
- scitex/plt/utils/metadata/_precision_config.py +68 -0
- scitex/plt/utils/metadata/_precision_sections.py +211 -0
- scitex/plt/utils/metadata/_recipe_extraction.py +267 -0
- scitex/plt/utils/metadata/_style_parsing.py +174 -0
- scitex/repro/_RandomStateManager.py +33 -38
- scitex/repro/__init__.py +16 -7
- scitex/repro/_gen_ID.py +7 -9
- scitex/repro/_gen_timestamp.py +7 -6
- scitex/repro/_hash_array.py +8 -12
- scitex/reproduce/__init__.py +1 -1
- scitex/resource/_get_processor_usages.py +3 -1
- scitex/resource/_log_processor_usages.py +3 -1
- scitex/rng/__init__.py +1 -1
- scitex/schema/README.md +178 -0
- scitex/schema/__init__.py +144 -0
- scitex/schema/_canvas.py +444 -0
- scitex/schema/_stats.py +762 -0
- scitex/schema/_validation.py +590 -0
- scitex/scholar/.legacy/Scholar.py +5 -12
- scitex/scholar/.legacy/_Scholar.py +66 -99
- scitex/scholar/.legacy/_ScholarAPI.py +75 -66
- scitex/scholar/.legacy/_tmp/search_engine/_BaseSearchEngine.py +3 -3
- scitex/scholar/.legacy/_tmp/search_engine/_UnifiedSearcher.py +4 -9
- scitex/scholar/.legacy/_tmp/search_engine/__init__.py +14 -21
- scitex/scholar/.legacy/_tmp/search_engine/local/_LocalSearchEngine.py +40 -37
- scitex/scholar/.legacy/_tmp/search_engine/local/_VectorSearchEngine.py +31 -28
- scitex/scholar/.legacy/_tmp/search_engine/web/_ArxivSearchEngine.py +74 -65
- scitex/scholar/.legacy/_tmp/search_engine/web/_CrossRefSearchEngine.py +122 -116
- scitex/scholar/.legacy/_tmp/search_engine/web/_GoogleScholarSearchEngine.py +65 -59
- scitex/scholar/.legacy/_tmp/search_engine/web/_PubMedSearchEngine.py +121 -107
- scitex/scholar/.legacy/_tmp/search_engine/web/_SemanticScholarSearchEngine.py +5 -12
- scitex/scholar/.legacy/database/_DatabaseEntry.py +49 -45
- scitex/scholar/.legacy/database/_DatabaseIndex.py +131 -94
- scitex/scholar/.legacy/database/_LibraryManager.py +65 -63
- scitex/scholar/.legacy/database/_PaperDatabase.py +138 -124
- scitex/scholar/.legacy/database/_ScholarDatabaseIntegration.py +14 -36
- scitex/scholar/.legacy/database/_StorageIntegratedDB.py +192 -156
- scitex/scholar/.legacy/database/_ZoteroCompatibleDB.py +300 -237
- scitex/scholar/.legacy/database/__init__.py +2 -1
- scitex/scholar/.legacy/database/manage.py +92 -84
- scitex/scholar/.legacy/lookup/_LookupIndex.py +157 -101
- scitex/scholar/.legacy/lookup/__init__.py +2 -1
- scitex/scholar/.legacy/metadata/doi/batch/_MetadataHandlerForBatchDOIResolution.py +4 -9
- scitex/scholar/.legacy/metadata/doi/batch/_ProgressManagerForBatchDOIResolution.py +10 -23
- scitex/scholar/.legacy/metadata/doi/batch/_SourceStatsManagerForBatchDOIResolution.py +4 -9
- scitex/scholar/.legacy/metadata/doi/batch/__init__.py +3 -1
- scitex/scholar/.legacy/metadata/doi/resolvers/_BatchDOIResolver.py +10 -25
- scitex/scholar/.legacy/metadata/doi/resolvers/_BibTeXDOIResolver.py +19 -49
- scitex/scholar/.legacy/metadata/doi/resolvers/_DOIResolver.py +1 -0
- scitex/scholar/.legacy/metadata/doi/resolvers/_SingleDOIResolver.py +8 -20
- scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
- scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +49 -37
- scitex/scholar/.legacy/metadata/doi/sources/_ArXivSource.py +11 -30
- scitex/scholar/.legacy/metadata/doi/sources/_BaseDOISource.py +19 -47
- scitex/scholar/.legacy/metadata/doi/sources/_CrossRefLocalSource.py +1 -0
- scitex/scholar/.legacy/metadata/doi/sources/_CrossRefSource.py +12 -33
- scitex/scholar/.legacy/metadata/doi/sources/_OpenAlexSource.py +8 -20
- scitex/scholar/.legacy/metadata/doi/sources/_PubMedSource.py +10 -27
- scitex/scholar/.legacy/metadata/doi/sources/_SemanticScholarSource.py +11 -29
- scitex/scholar/.legacy/metadata/doi/sources/_SourceManager.py +8 -21
- scitex/scholar/.legacy/metadata/doi/sources/_SourceResolutionStrategy.py +24 -55
- scitex/scholar/.legacy/metadata/doi/sources/_SourceRotationManager.py +8 -21
- scitex/scholar/.legacy/metadata/doi/sources/_URLDOISource.py +9 -16
- scitex/scholar/.legacy/metadata/doi/sources/_UnifiedSource.py +8 -22
- scitex/scholar/.legacy/metadata/doi/sources/__init__.py +1 -0
- scitex/scholar/.legacy/metadata/doi/utils/_PubMedConverter.py +4 -8
- scitex/scholar/.legacy/metadata/doi/utils/_RateLimitHandler.py +17 -43
- scitex/scholar/.legacy/metadata/doi/utils/_TextNormalizer.py +8 -18
- scitex/scholar/.legacy/metadata/doi/utils/_URLDOIExtractor.py +4 -8
- scitex/scholar/.legacy/metadata/doi/utils/__init__.py +1 -0
- scitex/scholar/.legacy/metadata/doi/utils/_to_complete_metadata_structure.py +1 -0
- scitex/scholar/.legacy/metadata/enrichment/_LibraryEnricher.py +2 -3
- scitex/scholar/.legacy/metadata/enrichment/enrichers/_ImpactFactorEnricher.py +6 -12
- scitex/scholar/.legacy/metadata/enrichment/enrichers/_SmartEnricher.py +5 -10
- scitex/scholar/.legacy/metadata/enrichment/sources/_UnifiedMetadataSource.py +4 -5
- scitex/scholar/.legacy/metadata/query_to_full_meta_json.py +8 -12
- scitex/scholar/.legacy/metadata/urls/_URLMetadataHandler.py +3 -3
- scitex/scholar/.legacy/metadata/urls/_ZoteroTranslatorRunner.py +15 -21
- scitex/scholar/.legacy/metadata/urls/__init__.py +3 -3
- scitex/scholar/.legacy/metadata/urls/_finder.py +4 -6
- scitex/scholar/.legacy/metadata/urls/_handler.py +7 -15
- scitex/scholar/.legacy/metadata/urls/_resolver.py +6 -12
- scitex/scholar/.legacy/search/_Embedder.py +74 -69
- scitex/scholar/.legacy/search/_SemanticSearch.py +91 -90
- scitex/scholar/.legacy/search/_SemanticSearchEngine.py +104 -109
- scitex/scholar/.legacy/search/_UnifiedSearcher.py +530 -471
- scitex/scholar/.legacy/search/_VectorDatabase.py +111 -92
- scitex/scholar/.legacy/search/__init__.py +1 -0
- scitex/scholar/.legacy/storage/_EnhancedStorageManager.py +182 -154
- scitex/scholar/.legacy/storage/__init__.py +2 -1
- scitex/scholar/__init__.py +0 -2
- scitex/scholar/__main__.py +1 -3
- scitex/scholar/auth/ScholarAuthManager.py +13 -36
- scitex/scholar/auth/core/AuthenticationGateway.py +15 -29
- scitex/scholar/auth/core/BrowserAuthenticator.py +22 -57
- scitex/scholar/auth/core/StrategyResolver.py +10 -27
- scitex/scholar/auth/core/__init__.py +5 -1
- scitex/scholar/auth/gateway/_OpenURLLinkFinder.py +11 -21
- scitex/scholar/auth/gateway/_OpenURLResolver.py +10 -18
- scitex/scholar/auth/gateway/_resolve_functions.py +3 -3
- scitex/scholar/auth/providers/BaseAuthenticator.py +1 -0
- scitex/scholar/auth/providers/EZProxyAuthenticator.py +7 -14
- scitex/scholar/auth/providers/OpenAthensAuthenticator.py +29 -57
- scitex/scholar/auth/providers/ShibbolethAuthenticator.py +87 -73
- scitex/scholar/auth/session/AuthCacheManager.py +12 -22
- scitex/scholar/auth/session/SessionManager.py +4 -6
- scitex/scholar/auth/sso/BaseSSOAutomator.py +13 -19
- scitex/scholar/auth/sso/OpenAthensSSOAutomator.py +16 -45
- scitex/scholar/auth/sso/SSOAutomator.py +8 -15
- scitex/scholar/auth/sso/UniversityOfMelbourneSSOAutomator.py +13 -23
- scitex/scholar/browser/ScholarBrowserManager.py +31 -56
- scitex/scholar/browser/__init__.py +1 -0
- scitex/scholar/browser/utils/click_and_wait.py +3 -4
- scitex/scholar/browser/utils/close_unwanted_pages.py +4 -7
- scitex/scholar/browser/utils/wait_redirects.py +15 -40
- scitex/scholar/citation_graph/__init__.py +0 -0
- scitex/scholar/citation_graph/builder.py +3 -7
- scitex/scholar/citation_graph/database.py +4 -11
- scitex/scholar/citation_graph/example.py +5 -10
- scitex/scholar/citation_graph/models.py +0 -0
- scitex/scholar/cli/_url_utils.py +1 -1
- scitex/scholar/cli/chrome.py +5 -3
- scitex/scholar/cli/download_pdf.py +13 -14
- scitex/scholar/cli/handlers/bibtex_handler.py +4 -12
- scitex/scholar/cli/handlers/doi_handler.py +1 -3
- scitex/scholar/cli/handlers/project_handler.py +6 -20
- scitex/scholar/cli/open_browser.py +41 -39
- scitex/scholar/cli/open_browser_auto.py +31 -39
- scitex/scholar/cli/open_browser_monitored.py +27 -24
- scitex/scholar/config/ScholarConfig.py +5 -8
- scitex/scholar/config/__init__.py +1 -0
- scitex/scholar/config/core/_CascadeConfig.py +3 -3
- scitex/scholar/config/core/_PathManager.py +16 -28
- scitex/scholar/core/Paper.py +79 -78
- scitex/scholar/core/Papers.py +16 -27
- scitex/scholar/core/Scholar.py +98 -229
- scitex/scholar/core/journal_normalizer.py +52 -49
- scitex/scholar/core/oa_cache.py +27 -23
- scitex/scholar/core/open_access.py +17 -8
- scitex/scholar/docs/template.py +4 -3
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/clf_svm.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/download.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_conf_mat.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_digits.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_umap_space.py +0 -0
- scitex/scholar/examples/00_config.py +10 -9
- scitex/scholar/examples/01_auth.py +3 -0
- scitex/scholar/examples/02_browser.py +14 -10
- scitex/scholar/examples/03_01-engine.py +3 -0
- scitex/scholar/examples/03_02-engine-for-bibtex.py +4 -3
- scitex/scholar/examples/04_01-url.py +9 -9
- scitex/scholar/examples/04_02-url-for-bibtex.py +7 -3
- scitex/scholar/examples/04_02-url-for-dois.py +87 -97
- scitex/scholar/examples/05_download_pdf.py +10 -4
- scitex/scholar/examples/06_find_and_download.py +6 -6
- scitex/scholar/examples/06_parse_bibtex.py +17 -17
- scitex/scholar/examples/07_storage_integration.py +6 -9
- scitex/scholar/examples/99_fullpipeline-for-bibtex.py +14 -15
- scitex/scholar/examples/99_fullpipeline-for-one-entry.py +31 -23
- scitex/scholar/examples/99_maintenance.py +3 -0
- scitex/scholar/examples/dev.py +2 -3
- scitex/scholar/examples/zotero_integration.py +11 -18
- scitex/scholar/impact_factor/ImpactFactorEngine.py +7 -9
- scitex/scholar/impact_factor/estimation/__init__.py +4 -4
- scitex/scholar/impact_factor/estimation/core/__init__.py +3 -7
- scitex/scholar/impact_factor/estimation/core/cache_manager.py +223 -211
- scitex/scholar/impact_factor/estimation/core/calculator.py +165 -131
- scitex/scholar/impact_factor/estimation/core/journal_matcher.py +217 -172
- scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py +6 -14
- scitex/scholar/impact_factor/jcr/build_database.py +4 -3
- scitex/scholar/integration/base.py +9 -17
- scitex/scholar/integration/mendeley/exporter.py +2 -4
- scitex/scholar/integration/mendeley/importer.py +3 -3
- scitex/scholar/integration/mendeley/linker.py +3 -3
- scitex/scholar/integration/mendeley/mapper.py +9 -6
- scitex/scholar/integration/zotero/__main__.py +26 -43
- scitex/scholar/integration/zotero/exporter.py +15 -11
- scitex/scholar/integration/zotero/importer.py +12 -10
- scitex/scholar/integration/zotero/linker.py +8 -12
- scitex/scholar/integration/zotero/mapper.py +17 -12
- scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
- scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +47 -35
- scitex/scholar/metadata_engines/ScholarEngine.py +21 -43
- scitex/scholar/metadata_engines/__init__.py +1 -0
- scitex/scholar/metadata_engines/individual/ArXivEngine.py +15 -37
- scitex/scholar/metadata_engines/individual/CrossRefEngine.py +15 -42
- scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py +24 -45
- scitex/scholar/metadata_engines/individual/OpenAlexEngine.py +11 -21
- scitex/scholar/metadata_engines/individual/PubMedEngine.py +10 -27
- scitex/scholar/metadata_engines/individual/SemanticScholarEngine.py +28 -35
- scitex/scholar/metadata_engines/individual/URLDOIEngine.py +11 -22
- scitex/scholar/metadata_engines/individual/_BaseDOIEngine.py +20 -49
- scitex/scholar/metadata_engines/utils/_PubMedConverter.py +4 -8
- scitex/scholar/metadata_engines/utils/_URLDOIExtractor.py +5 -10
- scitex/scholar/metadata_engines/utils/__init__.py +2 -0
- scitex/scholar/metadata_engines/utils/_metadata2bibtex.py +3 -0
- scitex/scholar/metadata_engines/utils/_standardize_metadata.py +2 -3
- scitex/scholar/pdf_download/ScholarPDFDownloader.py +25 -37
- scitex/scholar/pdf_download/strategies/chrome_pdf_viewer.py +11 -19
- scitex/scholar/pdf_download/strategies/direct_download.py +5 -9
- scitex/scholar/pdf_download/strategies/manual_download_fallback.py +3 -3
- scitex/scholar/pdf_download/strategies/manual_download_utils.py +6 -13
- scitex/scholar/pdf_download/strategies/open_access_download.py +49 -31
- scitex/scholar/pdf_download/strategies/response_body.py +8 -19
- scitex/scholar/pipelines/ScholarPipelineBibTeX.py +9 -18
- scitex/scholar/pipelines/ScholarPipelineMetadataParallel.py +25 -26
- scitex/scholar/pipelines/ScholarPipelineMetadataSingle.py +62 -23
- scitex/scholar/pipelines/ScholarPipelineParallel.py +13 -30
- scitex/scholar/pipelines/ScholarPipelineSearchParallel.py +299 -220
- scitex/scholar/pipelines/ScholarPipelineSearchSingle.py +202 -165
- scitex/scholar/pipelines/ScholarPipelineSingle.py +25 -51
- scitex/scholar/pipelines/SearchQueryParser.py +55 -55
- scitex/scholar/search_engines/ScholarSearchEngine.py +31 -27
- scitex/scholar/search_engines/_BaseSearchEngine.py +20 -23
- scitex/scholar/search_engines/individual/ArXivSearchEngine.py +53 -35
- scitex/scholar/search_engines/individual/CrossRefSearchEngine.py +47 -40
- scitex/scholar/search_engines/individual/OpenAlexSearchEngine.py +55 -50
- scitex/scholar/search_engines/individual/PubMedSearchEngine.py +8 -10
- scitex/scholar/search_engines/individual/SemanticScholarSearchEngine.py +55 -49
- scitex/scholar/storage/BibTeXHandler.py +150 -95
- scitex/scholar/storage/PaperIO.py +3 -6
- scitex/scholar/storage/ScholarLibrary.py +70 -49
- scitex/scholar/storage/_DeduplicationManager.py +52 -25
- scitex/scholar/storage/_LibraryCacheManager.py +19 -46
- scitex/scholar/storage/_LibraryManager.py +65 -175
- scitex/scholar/url_finder/ScholarURLFinder.py +9 -25
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_direct_links.py +1 -1
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_href.py +6 -10
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_navigation.py +4 -6
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_publisher_patterns.py +8 -15
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py +3 -3
- scitex/scholar/url_finder/strategies/find_supplementary_urls_by_href.py +3 -3
- scitex/scholar/url_finder/translators/core/patterns.py +6 -4
- scitex/scholar/url_finder/translators/core/registry.py +6 -9
- scitex/scholar/url_finder/translators/individual/BOFiP_Impots.py +60 -52
- scitex/scholar/url_finder/translators/individual/Baidu_Scholar.py +54 -62
- scitex/scholar/url_finder/translators/individual/Bangkok_Post.py +38 -44
- scitex/scholar/url_finder/translators/individual/Baruch_Foundation.py +43 -47
- scitex/scholar/url_finder/translators/individual/Beobachter.py +46 -50
- scitex/scholar/url_finder/translators/individual/Bezneng_Gajit.py +37 -41
- scitex/scholar/url_finder/translators/individual/BibLaTeX.py +59 -52
- scitex/scholar/url_finder/translators/individual/BibTeX.py +83 -79
- scitex/scholar/url_finder/translators/individual/Biblio_com.py +48 -51
- scitex/scholar/url_finder/translators/individual/Bibliontology_RDF.py +58 -56
- scitex/scholar/url_finder/translators/individual/Camara_Brasileira_do_Livro_ISBN.py +102 -99
- scitex/scholar/url_finder/translators/individual/CanLII.py +49 -43
- scitex/scholar/url_finder/translators/individual/Canada_com.py +36 -40
- scitex/scholar/url_finder/translators/individual/Canadian_Letters_and_Images.py +43 -43
- scitex/scholar/url_finder/translators/individual/Canadiana_ca.py +77 -66
- scitex/scholar/url_finder/translators/individual/Cascadilla_Proceedings_Project.py +68 -62
- scitex/scholar/url_finder/translators/individual/Central_and_Eastern_European_Online_Library_Journals.py +60 -60
- scitex/scholar/url_finder/translators/individual/Champlain_Society_Collection.py +63 -61
- scitex/scholar/url_finder/translators/individual/Chicago_Journal_of_Theoretical_Computer_Science.py +74 -58
- scitex/scholar/url_finder/translators/individual/Christian_Science_Monitor.py +32 -38
- scitex/scholar/url_finder/translators/individual/Columbia_University_Press.py +51 -47
- scitex/scholar/url_finder/translators/individual/Common_Place.py +66 -57
- scitex/scholar/url_finder/translators/individual/Cornell_LII.py +66 -62
- scitex/scholar/url_finder/translators/individual/Cornell_University_Press.py +38 -45
- scitex/scholar/url_finder/translators/individual/CourtListener.py +52 -56
- scitex/scholar/url_finder/translators/individual/DAI_Zenon.py +53 -54
- scitex/scholar/url_finder/translators/individual/access_medicine.py +27 -33
- scitex/scholar/url_finder/translators/individual/acm.py +1 -1
- scitex/scholar/url_finder/translators/individual/acm_digital_library.py +93 -63
- scitex/scholar/url_finder/translators/individual/airiti.py +3 -1
- scitex/scholar/url_finder/translators/individual/aosic.py +3 -1
- scitex/scholar/url_finder/translators/individual/archive_ouverte_aosic.py +3 -1
- scitex/scholar/url_finder/translators/individual/archive_ouverte_en_sciences_de_l_information_et_de_la_communication___aosic_.py +6 -2
- scitex/scholar/url_finder/translators/individual/artforum.py +35 -27
- scitex/scholar/url_finder/translators/individual/arxiv.py +1 -1
- scitex/scholar/url_finder/translators/individual/arxiv_org.py +8 -4
- scitex/scholar/url_finder/translators/individual/atlanta_journal_constitution.py +22 -18
- scitex/scholar/url_finder/translators/individual/atypon_journals.py +19 -11
- scitex/scholar/url_finder/translators/individual/austlii_and_nzlii.py +48 -44
- scitex/scholar/url_finder/translators/individual/australian_dictionary_of_biography.py +21 -17
- scitex/scholar/url_finder/translators/individual/bailii.py +22 -19
- scitex/scholar/url_finder/translators/individual/bbc.py +46 -42
- scitex/scholar/url_finder/translators/individual/bbc_genome.py +37 -25
- scitex/scholar/url_finder/translators/individual/biblioteca_nacional_de_maestros.py +24 -20
- scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationale_quebec_pistard.py +42 -43
- scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationales_quebec.py +87 -81
- scitex/scholar/url_finder/translators/individual/bibliotheque_nationale_france.py +39 -37
- scitex/scholar/url_finder/translators/individual/bibsys.py +32 -28
- scitex/scholar/url_finder/translators/individual/bioconductor.py +58 -52
- scitex/scholar/url_finder/translators/individual/biomed_central.py +23 -15
- scitex/scholar/url_finder/translators/individual/biorxiv.py +26 -13
- scitex/scholar/url_finder/translators/individual/blogger.py +39 -43
- scitex/scholar/url_finder/translators/individual/bloomberg.py +48 -52
- scitex/scholar/url_finder/translators/individual/bloomsbury_food_library.py +37 -37
- scitex/scholar/url_finder/translators/individual/bluesky.py +30 -28
- scitex/scholar/url_finder/translators/individual/bnf_isbn.py +1 -1
- scitex/scholar/url_finder/translators/individual/bocc.py +66 -60
- scitex/scholar/url_finder/translators/individual/boe.py +52 -52
- scitex/scholar/url_finder/translators/individual/brill.py +3 -1
- scitex/scholar/url_finder/translators/individual/business_standard.py +36 -38
- scitex/scholar/url_finder/translators/individual/cabi_cab_abstracts.py +39 -41
- scitex/scholar/url_finder/translators/individual/cambridge.py +3 -1
- scitex/scholar/url_finder/translators/individual/cambridge_core.py +30 -24
- scitex/scholar/url_finder/translators/individual/caod.py +50 -46
- scitex/scholar/url_finder/translators/individual/cbc.py +91 -67
- scitex/scholar/url_finder/translators/individual/ccfr_bnf.py +49 -53
- scitex/scholar/url_finder/translators/individual/cia_world_factbook.py +43 -33
- scitex/scholar/url_finder/translators/individual/crossref_rest.py +208 -174
- scitex/scholar/url_finder/translators/individual/current_affairs.py +29 -35
- scitex/scholar/url_finder/translators/individual/dabi.py +70 -66
- scitex/scholar/url_finder/translators/individual/dagens_nyheter.py +3 -1
- scitex/scholar/url_finder/translators/individual/dagstuhl.py +10 -15
- scitex/scholar/url_finder/translators/individual/dar_almandumah.py +13 -9
- scitex/scholar/url_finder/translators/individual/dart_europe.py +19 -22
- scitex/scholar/url_finder/translators/individual/data_gov.py +2 -2
- scitex/scholar/url_finder/translators/individual/databrary.py +27 -28
- scitex/scholar/url_finder/translators/individual/datacite_json.py +152 -137
- scitex/scholar/url_finder/translators/individual/dataverse.py +68 -64
- scitex/scholar/url_finder/translators/individual/daum_news.py +38 -38
- scitex/scholar/url_finder/translators/individual/dblp.py +4 -8
- scitex/scholar/url_finder/translators/individual/dblp_computer_science_bibliography.py +8 -3
- scitex/scholar/url_finder/translators/individual/dbpia.py +5 -3
- scitex/scholar/url_finder/translators/individual/defense_technical_information_center.py +30 -28
- scitex/scholar/url_finder/translators/individual/delpher.py +102 -79
- scitex/scholar/url_finder/translators/individual/demographic_research.py +35 -31
- scitex/scholar/url_finder/translators/individual/denik_cz.py +58 -54
- scitex/scholar/url_finder/translators/individual/depatisnet.py +7 -10
- scitex/scholar/url_finder/translators/individual/der_freitag.py +81 -66
- scitex/scholar/url_finder/translators/individual/der_spiegel.py +56 -54
- scitex/scholar/url_finder/translators/individual/digibib_net.py +3 -1
- scitex/scholar/url_finder/translators/individual/digizeitschriften.py +3 -1
- scitex/scholar/url_finder/translators/individual/dpla.py +13 -14
- scitex/scholar/url_finder/translators/individual/dspace.py +2 -2
- scitex/scholar/url_finder/translators/individual/ebrary.py +3 -1
- scitex/scholar/url_finder/translators/individual/ebscohost.py +3 -1
- scitex/scholar/url_finder/translators/individual/electronic_colloquium_on_computational_complexity.py +3 -1
- scitex/scholar/url_finder/translators/individual/elife.py +3 -1
- scitex/scholar/url_finder/translators/individual/elsevier_health_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/emerald.py +3 -1
- scitex/scholar/url_finder/translators/individual/emerald_insight.py +3 -1
- scitex/scholar/url_finder/translators/individual/epicurious.py +3 -1
- scitex/scholar/url_finder/translators/individual/eurogamerusgamer.py +3 -1
- scitex/scholar/url_finder/translators/individual/fachportal_padagogik.py +3 -1
- scitex/scholar/url_finder/translators/individual/frontiers.py +1 -1
- scitex/scholar/url_finder/translators/individual/gale_databases.py +3 -1
- scitex/scholar/url_finder/translators/individual/gms_german_medical_science.py +6 -2
- scitex/scholar/url_finder/translators/individual/ieee_computer_society.py +6 -2
- scitex/scholar/url_finder/translators/individual/ieee_xplore.py +41 -35
- scitex/scholar/url_finder/translators/individual/inter_research_science_center.py +6 -2
- scitex/scholar/url_finder/translators/individual/jisc_historical_texts.py +3 -1
- scitex/scholar/url_finder/translators/individual/jstor.py +14 -12
- scitex/scholar/url_finder/translators/individual/korean_national_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/la_times.py +3 -1
- scitex/scholar/url_finder/translators/individual/landesbibliographie_baden_wurttemberg.py +3 -1
- scitex/scholar/url_finder/translators/individual/legislative_insight.py +3 -1
- scitex/scholar/url_finder/translators/individual/libraries_tasmania.py +3 -1
- scitex/scholar/url_finder/translators/individual/library_catalog__koha_.py +3 -1
- scitex/scholar/url_finder/translators/individual/lingbuzz.py +2 -2
- scitex/scholar/url_finder/translators/individual/max_planck_institute_for_the_history_of_science_virtual_laboratory_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/mdpi.py +12 -6
- scitex/scholar/url_finder/translators/individual/microbiology_society_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/midas_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/nagoya_university_opac.py +3 -1
- scitex/scholar/url_finder/translators/individual/nature_publishing_group.py +32 -19
- scitex/scholar/url_finder/translators/individual/ntsb_accident_reports.py +3 -1
- scitex/scholar/url_finder/translators/individual/openedition_journals.py +8 -4
- scitex/scholar/url_finder/translators/individual/orcid.py +16 -15
- scitex/scholar/url_finder/translators/individual/oxford.py +25 -19
- scitex/scholar/url_finder/translators/individual/oxford_dictionaries_premium.py +3 -1
- scitex/scholar/url_finder/translators/individual/ozon_ru.py +3 -1
- scitex/scholar/url_finder/translators/individual/plos.py +9 -12
- scitex/scholar/url_finder/translators/individual/polygon.py +3 -1
- scitex/scholar/url_finder/translators/individual/primo.py +3 -1
- scitex/scholar/url_finder/translators/individual/project_muse.py +3 -1
- scitex/scholar/url_finder/translators/individual/pubfactory_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/pubmed.py +71 -65
- scitex/scholar/url_finder/translators/individual/pubmed_central.py +8 -6
- scitex/scholar/url_finder/translators/individual/rechtspraak_nl.py +3 -1
- scitex/scholar/url_finder/translators/individual/sage_journals.py +25 -17
- scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
- scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
- scitex/scholar/url_finder/translators/individual/sora.py +3 -1
- scitex/scholar/url_finder/translators/individual/springer.py +15 -11
- scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
- scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
- scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
- scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
- scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
- scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
- scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
- scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
- scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
- scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
- scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
- scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
- scitex/scholar/utils/text/_TextNormalizer.py +249 -176
- scitex/scholar/utils/validation/DOIValidator.py +31 -28
- scitex/scholar/utils/validation/__init__.py +0 -0
- scitex/scholar/utils/validation/validate_library_dois.py +61 -57
- scitex/scholar/zotero/__init__.py +1 -1
- scitex/security/cli.py +7 -20
- scitex/security/github.py +45 -32
- scitex/session/__init__.py +8 -9
- scitex/session/_decorator.py +49 -42
- scitex/session/_lifecycle.py +39 -39
- scitex/session/_manager.py +24 -20
- scitex/sh/__init__.py +4 -3
- scitex/sh/_execute.py +10 -7
- scitex/sh/_security.py +3 -3
- scitex/sh/_types.py +2 -3
- scitex/stats/__init__.py +57 -6
- scitex/stats/_schema.py +42 -569
- scitex/stats/auto/__init__.py +188 -0
- scitex/stats/auto/_context.py +331 -0
- scitex/stats/auto/_formatting.py +679 -0
- scitex/stats/auto/_rules.py +901 -0
- scitex/stats/auto/_selector.py +554 -0
- scitex/stats/auto/_styles.py +721 -0
- scitex/stats/correct/__init__.py +4 -4
- scitex/stats/correct/_correct_bonferroni.py +43 -34
- scitex/stats/correct/_correct_fdr.py +14 -40
- scitex/stats/correct/_correct_fdr_.py +39 -46
- scitex/stats/correct/_correct_holm.py +14 -32
- scitex/stats/correct/_correct_sidak.py +36 -21
- scitex/stats/descriptive/_circular.py +20 -21
- scitex/stats/descriptive/_describe.py +19 -5
- scitex/stats/descriptive/_nan.py +5 -7
- scitex/stats/descriptive/_real.py +4 -3
- scitex/stats/effect_sizes/__init__.py +10 -11
- scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
- scitex/stats/effect_sizes/_cohens_d.py +30 -31
- scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
- scitex/stats/effect_sizes/_eta_squared.py +23 -27
- scitex/stats/effect_sizes/_prob_superiority.py +18 -21
- scitex/stats/posthoc/__init__.py +3 -3
- scitex/stats/posthoc/_dunnett.py +75 -55
- scitex/stats/posthoc/_games_howell.py +61 -43
- scitex/stats/posthoc/_tukey_hsd.py +42 -34
- scitex/stats/power/__init__.py +2 -2
- scitex/stats/power/_power.py +56 -56
- scitex/stats/tests/__init__.py +1 -1
- scitex/stats/tests/correlation/__init__.py +1 -1
- scitex/stats/tests/correlation/_test_pearson.py +28 -38
- scitex/stats/utils/__init__.py +14 -17
- scitex/stats/utils/_effect_size.py +85 -78
- scitex/stats/utils/_formatters.py +49 -43
- scitex/stats/utils/_normalizers.py +7 -14
- scitex/stats/utils/_power.py +56 -56
- scitex/str/__init__.py +1 -0
- scitex/str/_clean_path.py +3 -3
- scitex/str/_factor_out_digits.py +86 -58
- scitex/str/_format_plot_text.py +180 -111
- scitex/str/_latex.py +19 -19
- scitex/str/_latex_fallback.py +9 -10
- scitex/str/_parse.py +3 -6
- scitex/str/_print_debug.py +13 -13
- scitex/str/_printc.py +2 -0
- scitex/str/_search.py +3 -3
- scitex/template/.legacy/_clone_project.py +9 -13
- scitex/template/__init__.py +10 -2
- scitex/template/_clone_project.py +7 -2
- scitex/template/_copy.py +1 -0
- scitex/template/_customize.py +3 -6
- scitex/template/_git_strategy.py +2 -3
- scitex/template/_rename.py +1 -0
- scitex/template/clone_pip_project.py +6 -7
- scitex/template/clone_research.py +7 -10
- scitex/template/clone_singularity.py +6 -7
- scitex/template/clone_writer_directory.py +6 -7
- scitex/tex/_preview.py +26 -11
- scitex/tex/_to_vec.py +10 -7
- scitex/torch/__init__.py +11 -1
- scitex/types/_ArrayLike.py +2 -0
- scitex/types/_is_listed_X.py +3 -3
- scitex/units.py +110 -77
- scitex/utils/_compress_hdf5.py +3 -3
- scitex/utils/_email.py +8 -4
- scitex/utils/_notify.py +14 -8
- scitex/utils/_search.py +6 -6
- scitex/utils/_verify_scitex_format.py +17 -42
- scitex/utils/_verify_scitex_format_v01.py +12 -34
- scitex/utils/template.py +4 -3
- scitex/vis/__init__.py +0 -0
- scitex/vis/backend/__init__.py +3 -3
- scitex/vis/backend/{export.py → _export.py} +1 -1
- scitex/vis/backend/{parser.py → _parser.py} +1 -3
- scitex/vis/backend/{render.py → _render.py} +1 -1
- scitex/vis/canvas.py +15 -3
- scitex/vis/editor/__init__.py +0 -0
- scitex/vis/editor/_dearpygui_editor.py +450 -304
- scitex/vis/editor/_defaults.py +114 -123
- scitex/vis/editor/_edit.py +38 -26
- scitex/vis/editor/_flask_editor.py +8 -8
- scitex/vis/editor/_mpl_editor.py +63 -48
- scitex/vis/editor/_qt_editor.py +210 -159
- scitex/vis/editor/_tkinter_editor.py +146 -89
- scitex/vis/editor/flask_editor/__init__.py +10 -10
- scitex/vis/editor/flask_editor/_bbox.py +529 -0
- scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
- scitex/vis/editor/flask_editor/_plotter.py +567 -0
- scitex/vis/editor/flask_editor/_renderer.py +393 -0
- scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
- scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
- scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
- scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
- scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
- scitex/vis/io/__init__.py +5 -5
- scitex/vis/io/{canvas.py → _canvas.py} +8 -4
- scitex/vis/io/{data.py → _data.py} +13 -9
- scitex/vis/io/{directory.py → _directory.py} +7 -4
- scitex/vis/io/{export.py → _export.py} +15 -12
- scitex/vis/io/{load.py → _load.py} +1 -1
- scitex/vis/io/{panel.py → _panel.py} +21 -13
- scitex/vis/io/{save.py → _save.py} +0 -0
- scitex/vis/model/__init__.py +7 -7
- scitex/vis/model/{annotations.py → _annotations.py} +2 -4
- scitex/vis/model/{axes.py → _axes.py} +1 -1
- scitex/vis/model/{figure.py → _figure.py} +0 -0
- scitex/vis/model/{guides.py → _guides.py} +1 -1
- scitex/vis/model/{plot.py → _plot.py} +2 -4
- scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
- scitex/vis/model/{styles.py → _styles.py} +0 -0
- scitex/vis/utils/__init__.py +2 -2
- scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
- scitex/vis/utils/{validate.py → _validate.py} +3 -9
- scitex/web/__init__.py +7 -1
- scitex/web/_scraping.py +54 -38
- scitex/web/_search_pubmed.py +30 -14
- scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
- scitex/writer/.legacy/_compile.py +18 -28
- scitex/writer/Writer.py +8 -21
- scitex/writer/__init__.py +11 -11
- scitex/writer/_clone_writer_project.py +2 -6
- scitex/writer/_compile/__init__.py +1 -0
- scitex/writer/_compile/_parser.py +1 -0
- scitex/writer/_compile/_runner.py +35 -38
- scitex/writer/_compile/_validator.py +1 -0
- scitex/writer/_compile/manuscript.py +1 -0
- scitex/writer/_compile/revision.py +1 -0
- scitex/writer/_compile/supplementary.py +1 -0
- scitex/writer/_compile_async.py +5 -12
- scitex/writer/_project/__init__.py +1 -0
- scitex/writer/_project/_create.py +10 -25
- scitex/writer/_project/_trees.py +4 -9
- scitex/writer/_project/_validate.py +2 -3
- scitex/writer/_validate_tree_structures.py +7 -18
- scitex/writer/dataclasses/__init__.py +8 -10
- scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
- scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
- scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
- scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
- scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
- scitex/writer/dataclasses/core/_Document.py +2 -3
- scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
- scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
- scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
- scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
- scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
- scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
- scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
- scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
- scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
- scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
- scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
- scitex/writer/utils/.legacy_git_retry.py +3 -8
- scitex/writer/utils/_parse_latex_logs.py +2 -3
- scitex/writer/utils/_parse_script_args.py +20 -23
- scitex/writer/utils/_watch.py +5 -5
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/METADATA +4 -10
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
- scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
- scitex/vis/editor/flask_editor/bbox.py +0 -216
- scitex/vis/editor/flask_editor/plotter.py +0 -130
- scitex/vis/editor/flask_editor/renderer.py +0 -184
- scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
scitex/cli/web.py
CHANGED
|
@@ -45,25 +45,25 @@ def web():
|
|
|
45
45
|
|
|
46
46
|
|
|
47
47
|
@web.command()
|
|
48
|
-
@click.argument(
|
|
48
|
+
@click.argument("url")
|
|
49
49
|
@click.option(
|
|
50
|
-
|
|
51
|
-
|
|
50
|
+
"--pattern",
|
|
51
|
+
"-p",
|
|
52
|
+
help='Regex pattern to filter URLs (e.g., "\\.pdf$" for PDF files)',
|
|
52
53
|
)
|
|
53
54
|
@click.option(
|
|
54
|
-
|
|
55
|
-
is_flag=True,
|
|
56
|
-
help='Only include URLs from the same domain'
|
|
55
|
+
"--same-domain", is_flag=True, help="Only include URLs from the same domain"
|
|
57
56
|
)
|
|
58
57
|
@click.option(
|
|
59
|
-
|
|
58
|
+
"--relative",
|
|
60
59
|
is_flag=True,
|
|
61
|
-
help=
|
|
60
|
+
help="Keep URLs as relative instead of converting to absolute",
|
|
62
61
|
)
|
|
63
62
|
@click.option(
|
|
64
|
-
|
|
63
|
+
"--output",
|
|
64
|
+
"-o",
|
|
65
65
|
type=click.Path(),
|
|
66
|
-
help=
|
|
66
|
+
help="Save URLs to file instead of printing to stdout",
|
|
67
67
|
)
|
|
68
68
|
def get_urls_cmd(url, pattern, same_domain, relative, output):
|
|
69
69
|
"""Extract all URLs from a webpage."""
|
|
@@ -71,23 +71,20 @@ def get_urls_cmd(url, pattern, same_domain, relative, output):
|
|
|
71
71
|
click.echo(f"Extracting URLs from: {url}")
|
|
72
72
|
|
|
73
73
|
urls = get_urls(
|
|
74
|
-
url,
|
|
75
|
-
pattern=pattern,
|
|
76
|
-
absolute=not relative,
|
|
77
|
-
same_domain=same_domain
|
|
74
|
+
url, pattern=pattern, absolute=not relative, same_domain=same_domain
|
|
78
75
|
)
|
|
79
76
|
|
|
80
77
|
if not urls:
|
|
81
|
-
click.secho("No URLs found", fg=
|
|
78
|
+
click.secho("No URLs found", fg="yellow")
|
|
82
79
|
sys.exit(0)
|
|
83
80
|
|
|
84
|
-
click.secho(f"Found {len(urls)} URLs", fg=
|
|
81
|
+
click.secho(f"Found {len(urls)} URLs", fg="green")
|
|
85
82
|
|
|
86
83
|
if output:
|
|
87
84
|
output_path = Path(output)
|
|
88
85
|
output_path.parent.mkdir(parents=True, exist_ok=True)
|
|
89
|
-
with open(output_path,
|
|
90
|
-
f.write(
|
|
86
|
+
with open(output_path, "w") as f:
|
|
87
|
+
f.write("\n".join(urls))
|
|
91
88
|
click.echo(f"URLs saved to: {output_path}")
|
|
92
89
|
else:
|
|
93
90
|
click.echo()
|
|
@@ -97,48 +94,42 @@ def get_urls_cmd(url, pattern, same_domain, relative, output):
|
|
|
97
94
|
sys.exit(0)
|
|
98
95
|
|
|
99
96
|
except Exception as e:
|
|
100
|
-
click.secho(f"ERROR: {e}", fg=
|
|
97
|
+
click.secho(f"ERROR: {e}", fg="red", err=True)
|
|
101
98
|
sys.exit(1)
|
|
102
99
|
|
|
103
100
|
|
|
104
101
|
@web.command()
|
|
105
|
-
@click.argument(
|
|
102
|
+
@click.argument("url")
|
|
106
103
|
@click.option(
|
|
107
|
-
|
|
108
|
-
help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
|
|
104
|
+
"--pattern", "-p", help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
|
|
109
105
|
)
|
|
110
106
|
@click.option(
|
|
111
|
-
|
|
112
|
-
is_flag=True,
|
|
113
|
-
help='Only include images from the same domain'
|
|
107
|
+
"--same-domain", is_flag=True, help="Only include images from the same domain"
|
|
114
108
|
)
|
|
115
109
|
@click.option(
|
|
116
|
-
|
|
110
|
+
"--output",
|
|
111
|
+
"-o",
|
|
117
112
|
type=click.Path(),
|
|
118
|
-
help=
|
|
113
|
+
help="Save image URLs to file instead of printing to stdout",
|
|
119
114
|
)
|
|
120
115
|
def get_image_urls_cmd(url, pattern, same_domain, output):
|
|
121
116
|
"""Extract image URLs from a webpage without downloading them."""
|
|
122
117
|
try:
|
|
123
118
|
click.echo(f"Extracting image URLs from: {url}")
|
|
124
119
|
|
|
125
|
-
img_urls = get_image_urls(
|
|
126
|
-
url,
|
|
127
|
-
pattern=pattern,
|
|
128
|
-
same_domain=same_domain
|
|
129
|
-
)
|
|
120
|
+
img_urls = get_image_urls(url, pattern=pattern, same_domain=same_domain)
|
|
130
121
|
|
|
131
122
|
if not img_urls:
|
|
132
|
-
click.secho("No image URLs found", fg=
|
|
123
|
+
click.secho("No image URLs found", fg="yellow")
|
|
133
124
|
sys.exit(0)
|
|
134
125
|
|
|
135
|
-
click.secho(f"Found {len(img_urls)} image URLs", fg=
|
|
126
|
+
click.secho(f"Found {len(img_urls)} image URLs", fg="green")
|
|
136
127
|
|
|
137
128
|
if output:
|
|
138
129
|
output_path = Path(output)
|
|
139
130
|
output_path.parent.mkdir(parents=True, exist_ok=True)
|
|
140
|
-
with open(output_path,
|
|
141
|
-
f.write(
|
|
131
|
+
with open(output_path, "w") as f:
|
|
132
|
+
f.write("\n".join(img_urls))
|
|
142
133
|
click.echo(f"Image URLs saved to: {output_path}")
|
|
143
134
|
else:
|
|
144
135
|
click.echo()
|
|
@@ -148,36 +139,34 @@ def get_image_urls_cmd(url, pattern, same_domain, output):
|
|
|
148
139
|
sys.exit(0)
|
|
149
140
|
|
|
150
141
|
except Exception as e:
|
|
151
|
-
click.secho(f"ERROR: {e}", fg=
|
|
142
|
+
click.secho(f"ERROR: {e}", fg="red", err=True)
|
|
152
143
|
sys.exit(1)
|
|
153
144
|
|
|
154
145
|
|
|
155
146
|
@web.command()
|
|
156
|
-
@click.argument(
|
|
147
|
+
@click.argument("url")
|
|
157
148
|
@click.option(
|
|
158
|
-
|
|
149
|
+
"--output",
|
|
150
|
+
"-o",
|
|
159
151
|
type=click.Path(),
|
|
160
|
-
help=
|
|
152
|
+
help="Output directory (default: $SCITEX_WEB_DOWNLOADS_DIR or $SCITEX_DIR/web/downloads)",
|
|
161
153
|
)
|
|
162
154
|
@click.option(
|
|
163
|
-
|
|
164
|
-
help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
|
|
155
|
+
"--pattern", "-p", help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
|
|
165
156
|
)
|
|
166
157
|
@click.option(
|
|
167
|
-
|
|
168
|
-
default=
|
|
169
|
-
help=
|
|
158
|
+
"--min-size",
|
|
159
|
+
default="100x100",
|
|
160
|
+
help="Minimum image size as WIDTHxHEIGHT (default: 100x100)",
|
|
170
161
|
)
|
|
171
162
|
@click.option(
|
|
172
|
-
|
|
173
|
-
is_flag=True,
|
|
174
|
-
help='Only download images from the same domain'
|
|
163
|
+
"--same-domain", is_flag=True, help="Only download images from the same domain"
|
|
175
164
|
)
|
|
176
165
|
@click.option(
|
|
177
|
-
|
|
166
|
+
"--max-workers",
|
|
178
167
|
type=int,
|
|
179
168
|
default=5,
|
|
180
|
-
help=
|
|
169
|
+
help="Number of concurrent download threads (default: 5)",
|
|
181
170
|
)
|
|
182
171
|
def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers):
|
|
183
172
|
"""
|
|
@@ -202,13 +191,13 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
|
|
|
202
191
|
min_size_tuple = None
|
|
203
192
|
if min_size:
|
|
204
193
|
try:
|
|
205
|
-
width, height = map(int, min_size.split(
|
|
194
|
+
width, height = map(int, min_size.split("x"))
|
|
206
195
|
min_size_tuple = (width, height)
|
|
207
196
|
except ValueError:
|
|
208
197
|
click.secho(
|
|
209
198
|
f"ERROR: Invalid min-size format. Use WIDTHxHEIGHT (e.g., '100x100')",
|
|
210
|
-
fg=
|
|
211
|
-
err=True
|
|
199
|
+
fg="red",
|
|
200
|
+
err=True,
|
|
212
201
|
)
|
|
213
202
|
sys.exit(1)
|
|
214
203
|
|
|
@@ -218,11 +207,11 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
|
|
|
218
207
|
pattern=pattern,
|
|
219
208
|
min_size=min_size_tuple,
|
|
220
209
|
max_workers=max_workers,
|
|
221
|
-
same_domain=same_domain
|
|
210
|
+
same_domain=same_domain,
|
|
222
211
|
)
|
|
223
212
|
|
|
224
213
|
if not paths:
|
|
225
|
-
click.secho("No images downloaded", fg=
|
|
214
|
+
click.secho("No images downloaded", fg="yellow")
|
|
226
215
|
sys.exit(0)
|
|
227
216
|
|
|
228
217
|
# Show where images were saved (get actual directory from first path)
|
|
@@ -231,37 +220,34 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
|
|
|
231
220
|
else:
|
|
232
221
|
actual_output = output or _get_default_download_dir()
|
|
233
222
|
|
|
234
|
-
click.secho(f"Successfully downloaded {len(paths)} images", fg=
|
|
223
|
+
click.secho(f"Successfully downloaded {len(paths)} images", fg="green")
|
|
235
224
|
click.echo(f"Images saved to: {actual_output}")
|
|
236
225
|
|
|
237
226
|
sys.exit(0)
|
|
238
227
|
|
|
239
228
|
except Exception as e:
|
|
240
|
-
click.secho(f"ERROR: {e}", fg=
|
|
229
|
+
click.secho(f"ERROR: {e}", fg="red", err=True)
|
|
241
230
|
sys.exit(1)
|
|
242
231
|
|
|
243
232
|
|
|
244
233
|
@web.command()
|
|
245
|
-
@click.argument(
|
|
234
|
+
@click.argument("url")
|
|
246
235
|
@click.option(
|
|
247
|
-
|
|
236
|
+
"--output",
|
|
237
|
+
"-o",
|
|
248
238
|
type=click.Path(),
|
|
249
|
-
help=
|
|
239
|
+
help="Output directory for the screenshot (default: ~/.scitex/capture)",
|
|
250
240
|
)
|
|
251
241
|
@click.option(
|
|
252
|
-
|
|
253
|
-
help='Optional message to include in the screenshot filename'
|
|
242
|
+
"--message", "-m", help="Optional message to include in the screenshot filename"
|
|
254
243
|
)
|
|
255
244
|
@click.option(
|
|
256
|
-
|
|
257
|
-
type=int,
|
|
258
|
-
default=85,
|
|
259
|
-
help='JPEG quality 1-100 (default: 85)'
|
|
245
|
+
"--quality", "-q", type=int, default=85, help="JPEG quality 1-100 (default: 85)"
|
|
260
246
|
)
|
|
261
247
|
@click.option(
|
|
262
|
-
|
|
248
|
+
"--full-page",
|
|
263
249
|
is_flag=True,
|
|
264
|
-
help=
|
|
250
|
+
help="Capture the full page (scrolling) instead of just viewport",
|
|
265
251
|
)
|
|
266
252
|
def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
267
253
|
"""
|
|
@@ -309,11 +295,7 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
|
309
295
|
|
|
310
296
|
# Use playwright MCP server to take screenshot
|
|
311
297
|
# We'll use a simple approach: navigate to URL and take screenshot
|
|
312
|
-
cmd = [
|
|
313
|
-
'playwright', 'screenshot',
|
|
314
|
-
url,
|
|
315
|
-
str(output_file)
|
|
316
|
-
]
|
|
298
|
+
cmd = ["playwright", "screenshot", url, str(output_file)]
|
|
317
299
|
|
|
318
300
|
# Try using the MCP approach first, fall back to direct playwright if available
|
|
319
301
|
try:
|
|
@@ -329,15 +311,18 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
|
329
311
|
await page.screenshot(
|
|
330
312
|
path=str(output_file),
|
|
331
313
|
full_page=full_page,
|
|
332
|
-
type=
|
|
333
|
-
quality=quality
|
|
314
|
+
type="png" if str(output_file).endswith(".png") else "jpeg",
|
|
315
|
+
quality=quality
|
|
316
|
+
if str(output_file).endswith(".jpg")
|
|
317
|
+
or str(output_file).endswith(".jpeg")
|
|
318
|
+
else None,
|
|
334
319
|
)
|
|
335
320
|
await browser.close()
|
|
336
321
|
|
|
337
322
|
asyncio.run(capture())
|
|
338
323
|
|
|
339
324
|
if output_file.exists():
|
|
340
|
-
click.secho(f"Screenshot saved successfully", fg=
|
|
325
|
+
click.secho(f"Screenshot saved successfully", fg="green")
|
|
341
326
|
click.echo(f"Location: {output_file}")
|
|
342
327
|
sys.exit(0)
|
|
343
328
|
else:
|
|
@@ -345,15 +330,17 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
|
345
330
|
|
|
346
331
|
except ImportError:
|
|
347
332
|
# Fall back to using playwright CLI if the Python package is not available
|
|
348
|
-
click.secho(
|
|
333
|
+
click.secho(
|
|
334
|
+
"Playwright Python package not found, trying CLI...", fg="yellow"
|
|
335
|
+
)
|
|
349
336
|
result = subprocess.run(
|
|
350
|
-
[
|
|
337
|
+
["playwright", "screenshot", url, str(output_file)],
|
|
351
338
|
capture_output=True,
|
|
352
|
-
text=True
|
|
339
|
+
text=True,
|
|
353
340
|
)
|
|
354
341
|
|
|
355
342
|
if result.returncode == 0 and output_file.exists():
|
|
356
|
-
click.secho(f"Screenshot saved successfully", fg=
|
|
343
|
+
click.secho(f"Screenshot saved successfully", fg="green")
|
|
357
344
|
click.echo(f"Location: {output_file}")
|
|
358
345
|
sys.exit(0)
|
|
359
346
|
else:
|
|
@@ -361,17 +348,24 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
|
361
348
|
|
|
362
349
|
except Exception as e:
|
|
363
350
|
error_msg = str(e)
|
|
364
|
-
click.secho(f"ERROR: {error_msg}", fg=
|
|
351
|
+
click.secho(f"ERROR: {error_msg}", fg="red", err=True)
|
|
365
352
|
click.echo()
|
|
366
353
|
|
|
367
354
|
# Provide context-specific troubleshooting
|
|
368
355
|
if "ERR_CONNECTION_REFUSED" in error_msg or "Connection refused" in error_msg:
|
|
369
356
|
click.echo("Troubleshooting - Connection Refused:")
|
|
370
357
|
click.echo(" 1. Make sure a web server is running at the specified URL")
|
|
371
|
-
click.echo(
|
|
358
|
+
click.echo(
|
|
359
|
+
" 2. Check if the port is correct (e.g., http://127.0.0.1:8000/)"
|
|
360
|
+
)
|
|
372
361
|
click.echo(" 3. Verify the server is accessible: curl <url>")
|
|
373
|
-
click.echo(
|
|
374
|
-
|
|
362
|
+
click.echo(
|
|
363
|
+
" 4. If using WSL, you may need to use the WSL IP instead of 127.0.0.1"
|
|
364
|
+
)
|
|
365
|
+
elif (
|
|
366
|
+
"ERR_NAME_NOT_RESOLVED" in error_msg
|
|
367
|
+
or "Name or service not known" in error_msg
|
|
368
|
+
):
|
|
375
369
|
click.echo("Troubleshooting - DNS Resolution Failed:")
|
|
376
370
|
click.echo(" 1. Check if the domain name is correct")
|
|
377
371
|
click.echo(" 2. Verify internet connection")
|
|
@@ -385,7 +379,10 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
|
385
379
|
click.echo("Troubleshooting - Playwright Not Installed:")
|
|
386
380
|
click.echo(" 1. Install Playwright: pip install playwright")
|
|
387
381
|
click.echo(" 2. Install browsers: playwright install chromium")
|
|
388
|
-
elif
|
|
382
|
+
elif (
|
|
383
|
+
"Executable doesn't exist" in error_msg
|
|
384
|
+
or "browser executable" in error_msg.lower()
|
|
385
|
+
):
|
|
389
386
|
click.echo("Troubleshooting - Browser Not Installed:")
|
|
390
387
|
click.echo(" 1. Install Chromium browser: playwright install chromium")
|
|
391
388
|
click.echo(" 2. Or install all browsers: playwright install")
|
|
@@ -399,11 +396,11 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
|
|
|
399
396
|
|
|
400
397
|
|
|
401
398
|
# Register command aliases
|
|
402
|
-
web.add_command(get_urls_cmd, name=
|
|
403
|
-
web.add_command(get_image_urls_cmd, name=
|
|
404
|
-
web.add_command(download_images_cmd, name=
|
|
405
|
-
web.add_command(take_screenshot_cmd, name=
|
|
399
|
+
web.add_command(get_urls_cmd, name="get-urls")
|
|
400
|
+
web.add_command(get_image_urls_cmd, name="get-image-urls")
|
|
401
|
+
web.add_command(download_images_cmd, name="download-images")
|
|
402
|
+
web.add_command(take_screenshot_cmd, name="take-screenshot")
|
|
406
403
|
|
|
407
404
|
|
|
408
|
-
if __name__ ==
|
|
405
|
+
if __name__ == "__main__":
|
|
409
406
|
web()
|
scitex/cli/writer.py
CHANGED
|
@@ -11,7 +11,7 @@ import sys
|
|
|
11
11
|
from pathlib import Path
|
|
12
12
|
|
|
13
13
|
|
|
14
|
-
@click.group(context_settings={
|
|
14
|
+
@click.group(context_settings={"help_option_names": ["-h", "--help"]})
|
|
15
15
|
def writer():
|
|
16
16
|
"""
|
|
17
17
|
Manuscript writing and LaTeX compilation
|
|
@@ -27,21 +27,16 @@ def writer():
|
|
|
27
27
|
|
|
28
28
|
|
|
29
29
|
@writer.command()
|
|
30
|
-
@click.argument(
|
|
30
|
+
@click.argument("project_dir", type=click.Path())
|
|
31
31
|
@click.option(
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
)
|
|
37
|
-
@click.option(
|
|
38
|
-
'--branch', '-b',
|
|
39
|
-
help='Specific branch of template to clone'
|
|
40
|
-
)
|
|
41
|
-
@click.option(
|
|
42
|
-
'--tag', '-t',
|
|
43
|
-
help='Specific tag/release of template to clone'
|
|
32
|
+
"--git-strategy",
|
|
33
|
+
"-g",
|
|
34
|
+
type=click.Choice(["child", "parent", "origin", "none"], case_sensitive=False),
|
|
35
|
+
default="child",
|
|
36
|
+
help="Git initialization strategy (default: child)",
|
|
44
37
|
)
|
|
38
|
+
@click.option("--branch", "-b", help="Specific branch of template to clone")
|
|
39
|
+
@click.option("--tag", "-t", help="Specific tag/release of template to clone")
|
|
45
40
|
def clone(project_dir, git_strategy, branch, tag):
|
|
46
41
|
"""
|
|
47
42
|
Clone a new writer project from template
|
|
@@ -74,7 +69,7 @@ def clone(project_dir, git_strategy, branch, tag):
|
|
|
74
69
|
sys.exit(1)
|
|
75
70
|
|
|
76
71
|
# Convert git_strategy 'none' to None
|
|
77
|
-
if git_strategy and git_strategy.lower() ==
|
|
72
|
+
if git_strategy and git_strategy.lower() == "none":
|
|
78
73
|
git_strategy = None
|
|
79
74
|
|
|
80
75
|
click.echo(f"Cloning writer project: {project_dir}")
|
|
@@ -90,11 +85,16 @@ def clone(project_dir, git_strategy, branch, tag):
|
|
|
90
85
|
if result:
|
|
91
86
|
project_path = Path(project_dir)
|
|
92
87
|
click.echo()
|
|
93
|
-
click.secho(
|
|
88
|
+
click.secho(
|
|
89
|
+
f"✓ Successfully cloned project at {project_path.absolute()}",
|
|
90
|
+
fg="green",
|
|
91
|
+
)
|
|
94
92
|
click.echo()
|
|
95
93
|
click.echo("Project structure:")
|
|
96
94
|
click.echo(f" {project_dir}/")
|
|
97
|
-
click.echo(
|
|
95
|
+
click.echo(
|
|
96
|
+
f" ├── 00_shared/ # Shared resources (figures, bibliography)"
|
|
97
|
+
)
|
|
98
98
|
click.echo(f" ├── 01_manuscript/ # Main manuscript")
|
|
99
99
|
click.echo(f" ├── 02_supplementary/ # Supplementary materials")
|
|
100
100
|
click.echo(f" ├── 03_revision/ # Revision documents")
|
|
@@ -105,35 +105,36 @@ def clone(project_dir, git_strategy, branch, tag):
|
|
|
105
105
|
click.echo(f" # Edit your manuscript in 01_manuscript/contents/")
|
|
106
106
|
click.echo(f" scitex writer compile manuscript")
|
|
107
107
|
else:
|
|
108
|
-
click.secho(f"✗ Failed to clone project", fg=
|
|
108
|
+
click.secho(f"✗ Failed to clone project", fg="red", err=True)
|
|
109
109
|
sys.exit(1)
|
|
110
110
|
|
|
111
111
|
except Exception as e:
|
|
112
|
-
click.secho(f"Error: {e}", fg=
|
|
112
|
+
click.secho(f"Error: {e}", fg="red", err=True)
|
|
113
113
|
sys.exit(1)
|
|
114
114
|
|
|
115
115
|
|
|
116
116
|
@writer.command()
|
|
117
117
|
@click.argument(
|
|
118
|
-
|
|
119
|
-
type=click.Choice(
|
|
120
|
-
|
|
118
|
+
"document",
|
|
119
|
+
type=click.Choice(
|
|
120
|
+
["manuscript", "supplementary", "revision"], case_sensitive=False
|
|
121
|
+
),
|
|
122
|
+
default="manuscript",
|
|
121
123
|
)
|
|
122
124
|
@click.option(
|
|
123
|
-
|
|
125
|
+
"--dir",
|
|
126
|
+
"-d",
|
|
124
127
|
type=click.Path(exists=True),
|
|
125
|
-
help=
|
|
128
|
+
help="Project directory (defaults to current directory)",
|
|
126
129
|
)
|
|
127
130
|
@click.option(
|
|
128
|
-
|
|
129
|
-
is_flag=True,
|
|
130
|
-
help='Enable change tracking (revision only)'
|
|
131
|
+
"--track-changes", is_flag=True, help="Enable change tracking (revision only)"
|
|
131
132
|
)
|
|
132
133
|
@click.option(
|
|
133
|
-
|
|
134
|
+
"--timeout",
|
|
134
135
|
type=int,
|
|
135
136
|
default=300,
|
|
136
|
-
help=
|
|
137
|
+
help="Compilation timeout in seconds (default: 300)",
|
|
137
138
|
)
|
|
138
139
|
def compile(document, dir, track_changes, timeout):
|
|
139
140
|
"""
|
|
@@ -160,21 +161,24 @@ def compile(document, dir, track_changes, timeout):
|
|
|
160
161
|
click.echo()
|
|
161
162
|
|
|
162
163
|
# Compile based on document type
|
|
163
|
-
if document ==
|
|
164
|
+
if document == "manuscript":
|
|
164
165
|
result = writer.compile_manuscript(timeout=timeout)
|
|
165
|
-
elif document ==
|
|
166
|
+
elif document == "supplementary":
|
|
166
167
|
result = writer.compile_supplementary(timeout=timeout)
|
|
167
|
-
elif document ==
|
|
168
|
+
elif document == "revision":
|
|
168
169
|
result = writer.compile_revision(
|
|
169
|
-
track_changes=track_changes,
|
|
170
|
-
timeout=timeout
|
|
170
|
+
track_changes=track_changes, timeout=timeout
|
|
171
171
|
)
|
|
172
172
|
|
|
173
173
|
if result.success:
|
|
174
|
-
click.secho(f"✓ Compilation successful!", fg=
|
|
174
|
+
click.secho(f"✓ Compilation successful!", fg="green")
|
|
175
175
|
click.echo(f"PDF: {result.output_pdf}")
|
|
176
176
|
else:
|
|
177
|
-
click.secho(
|
|
177
|
+
click.secho(
|
|
178
|
+
f"✗ Compilation failed (exit code {result.exit_code})",
|
|
179
|
+
fg="red",
|
|
180
|
+
err=True,
|
|
181
|
+
)
|
|
178
182
|
if result.errors:
|
|
179
183
|
click.echo()
|
|
180
184
|
click.echo("Errors:")
|
|
@@ -183,15 +187,16 @@ def compile(document, dir, track_changes, timeout):
|
|
|
183
187
|
sys.exit(result.exit_code)
|
|
184
188
|
|
|
185
189
|
except Exception as e:
|
|
186
|
-
click.secho(f"Error: {e}", fg=
|
|
190
|
+
click.secho(f"Error: {e}", fg="red", err=True)
|
|
187
191
|
sys.exit(1)
|
|
188
192
|
|
|
189
193
|
|
|
190
194
|
@writer.command()
|
|
191
195
|
@click.option(
|
|
192
|
-
|
|
196
|
+
"--dir",
|
|
197
|
+
"-d",
|
|
193
198
|
type=click.Path(exists=True),
|
|
194
|
-
help=
|
|
199
|
+
help="Project directory (defaults to current directory)",
|
|
195
200
|
)
|
|
196
201
|
def info(dir):
|
|
197
202
|
"""
|
|
@@ -220,23 +225,24 @@ def info(dir):
|
|
|
220
225
|
|
|
221
226
|
# Check for compiled PDFs
|
|
222
227
|
click.echo("Compiled PDFs:")
|
|
223
|
-
for doc_type in [
|
|
228
|
+
for doc_type in ["manuscript", "supplementary", "revision"]:
|
|
224
229
|
pdf = writer.get_pdf(doc_type)
|
|
225
230
|
if pdf:
|
|
226
|
-
click.secho(f" ✓ {doc_type}: {pdf}", fg=
|
|
231
|
+
click.secho(f" ✓ {doc_type}: {pdf}", fg="green")
|
|
227
232
|
else:
|
|
228
233
|
click.echo(f" - {doc_type}: not compiled")
|
|
229
234
|
|
|
230
235
|
except Exception as e:
|
|
231
|
-
click.secho(f"Error: {e}", fg=
|
|
236
|
+
click.secho(f"Error: {e}", fg="red", err=True)
|
|
232
237
|
sys.exit(1)
|
|
233
238
|
|
|
234
239
|
|
|
235
240
|
@writer.command()
|
|
236
241
|
@click.option(
|
|
237
|
-
|
|
242
|
+
"--dir",
|
|
243
|
+
"-d",
|
|
238
244
|
type=click.Path(exists=True),
|
|
239
|
-
help=
|
|
245
|
+
help="Project directory (defaults to current directory)",
|
|
240
246
|
)
|
|
241
247
|
def watch(dir):
|
|
242
248
|
"""
|
|
@@ -263,7 +269,7 @@ def watch(dir):
|
|
|
263
269
|
click.echo()
|
|
264
270
|
click.echo("Stopped watching")
|
|
265
271
|
except Exception as e:
|
|
266
|
-
click.secho(f"Error: {e}", fg=
|
|
272
|
+
click.secho(f"Error: {e}", fg="red", err=True)
|
|
267
273
|
sys.exit(1)
|
|
268
274
|
|
|
269
275
|
|
scitex/cloud/__init__.py
CHANGED
|
@@ -12,21 +12,23 @@ from typing import Optional
|
|
|
12
12
|
|
|
13
13
|
def is_cloud_environment() -> bool:
|
|
14
14
|
"""Check if running in SciTeX Cloud environment."""
|
|
15
|
-
return os.environ.get(
|
|
15
|
+
return os.environ.get("SCITEX_CLOUD_CODE_WORKSPACE") == "true"
|
|
16
16
|
|
|
17
17
|
|
|
18
18
|
def get_cloud_backend() -> str:
|
|
19
19
|
"""Get the cloud backend type."""
|
|
20
|
-
return os.environ.get(
|
|
20
|
+
return os.environ.get("SCITEX_CLOUD_CODE_BACKEND", "default")
|
|
21
21
|
|
|
22
22
|
|
|
23
23
|
def get_project_root() -> Optional[Path]:
|
|
24
24
|
"""Get the project root directory."""
|
|
25
|
-
project_root = os.environ.get(
|
|
25
|
+
project_root = os.environ.get("SCITEX_CLOUD_CODE_PROJECT_ROOT")
|
|
26
26
|
return Path(project_root) if project_root else None
|
|
27
27
|
|
|
28
28
|
|
|
29
|
-
def emit_inline_image(
|
|
29
|
+
def emit_inline_image(
|
|
30
|
+
image_path: str, alt_text: str = "Figure", width: int = 600
|
|
31
|
+
) -> None:
|
|
30
32
|
"""
|
|
31
33
|
Emit inline image marker for terminal display using iTerm2 protocol.
|
|
32
34
|
|
|
@@ -45,7 +47,7 @@ def emit_inline_image(image_path: str, alt_text: str = "Figure", width: int = 60
|
|
|
45
47
|
return
|
|
46
48
|
|
|
47
49
|
backend = get_cloud_backend()
|
|
48
|
-
if backend !=
|
|
50
|
+
if backend != "inline":
|
|
49
51
|
return
|
|
50
52
|
|
|
51
53
|
# Convert to absolute path if relative
|
|
@@ -73,11 +75,12 @@ def emit_inline_image(image_path: str, alt_text: str = "Figure", width: int = 60
|
|
|
73
75
|
display_path = image_path
|
|
74
76
|
|
|
75
77
|
# Emit marker that terminal consumer will detect
|
|
76
|
-
print(f
|
|
78
|
+
print(f"\n[SCITEX_IMAGE:{display_path}:{width}:{alt_text}]\n", flush=True)
|
|
77
79
|
|
|
78
80
|
except Exception as e:
|
|
79
81
|
print(f"Error displaying inline image: {e}", file=sys.stderr)
|
|
80
82
|
import traceback
|
|
83
|
+
|
|
81
84
|
traceback.print_exc(file=sys.stderr)
|
|
82
85
|
|
|
83
86
|
|
|
@@ -113,11 +116,11 @@ def emit_file_link(file_path: str, line_number: Optional[int] = None) -> None:
|
|
|
113
116
|
|
|
114
117
|
|
|
115
118
|
__all__ = [
|
|
116
|
-
|
|
117
|
-
|
|
118
|
-
|
|
119
|
-
|
|
120
|
-
|
|
119
|
+
"is_cloud_environment",
|
|
120
|
+
"get_cloud_backend",
|
|
121
|
+
"get_project_root",
|
|
122
|
+
"emit_inline_image",
|
|
123
|
+
"emit_file_link",
|
|
121
124
|
]
|
|
122
125
|
|
|
123
126
|
# Auto-import matplotlib hook to enable inline plotting
|